Pinkie Pie: Schism: Rainbow Dash accidentally catches Pinkie Pie in an unguarded moment, discovering an uncomfortable secret — and as we all know, spilling a secret is the fastest way to lose a friend FOREVER!

Rainbow Dash: Dependence: Dash turns to Fluttershy for help relaxing, but the cure may be worse than the original problem...

Applejack: Exposure: Applejack takes a lot of pride in being honest, but when that honesty extends to sharing all her feelings, complications quickly ensue.

Rarity: Loss: Rarity may be generous, but all her giving has a hidden cost — and that's becoming too much to bear.

Twilight Sparkle: Spellbound: As her friends' struggles with their personal problems reaches the breaking point, Twilight learns an Awful Truth from her mentor, one she must come to terms with if she's to have any hope of helping anyone.

In addition, the series has several side stories:

Alicorns: Blame: The truth behind the thousand year-schism between the Princesses comes to light, and is considerably more complex than the old fable of "The Mare in the Moon".

Ditzy Doo: Muffins: What is it with Ponyville's walleyed mailmare? Why does she have a unicorn foal? What does her Cutie Mark mean? And why is she so fixated on muffins? Is she an amnesiac CIA agent or something?

Trixie: Treasure: The once Great and Powerful Trixie comes into possession of the means to get back at the residents of Ponyville - but is she ready to pay the price for that vengeance?

A sequel, "Secrets and Lies", has been completed. Set after the end of Season Two, it leads off with a bang when Twilight is forced to kill Topsy Turvy/Screwball in self-defense. Having to hide that from the others leads to problems.

Aren't You Going to Ravish Me?: At one point, Rarity assumes that the Mayor's hints about taking a bribe to turn a blind eye to her unpaid taxes mean something entirely different. When she realizes the truth, all her horror and shock at her assumption being proven wrong is directed inward.

Granted, that was how Big Macintosh got a tax break.

The Atoner: Bright Eyes, who adopted a foal orphaned when she failed to protect her parents from Giovanni's hitpony.

Awful Truth: In Spellbound, the various reveals about the nature of the Elements of Harmony.

Averted: Word of God claims that Luna version was a lie and Celestia's is the truth

Black Magic: Twilight is forced to use Neighcromancy to save Dash's life.

Brainwashed and Crazy: In Treasure, Trixie uses the glamor of Celestia's Regalia to inflict this upon all of Ponyvile, save for Twilight, Snips and Snails.

Defeat Means Friendship: Once Trixie admitted that she'd acted like a world-class jerk because her feelings were hurt, she apologized to Celestia and went back home to learn a new act.

Empathic Weapon: The Regalia of the Daymare, which is linked to the Elements of Harmony and really dislikes having its powers abused by the wearer for their own selfish ends.

Epiphany Therapy: How Twilight tries to help her friends in the second half of Spellbound.

How Celestia and her royal guard show Twilight she's a living avatar of magic. "Kill her." (Cue horrified Twilight face and cliffhanger ending.)

Evil Cannot Comprehend Good: In Treasure, Trixie is mystified upon sensing that Fluttershy would have been just as compassionate towards her without the Regalia's glamor forcing her to submit.

The Evils of Free Will: In Treasure, Twilight Sparkle is struck by the thought that Pinkie Pie was finally freed of her depression and made truly happy by losing her free will. It's a sobering thought, and one that makes her submit to being taken back to Trixie.

Fantasy Counterpart Culture: Stalliongrad might be the most prominent example, that with a royal visit from tsarevna in Spellbound (and with perfect Russian to boot). Then there are mentionings of Xiao Ma, San Caballo and Puledria.

Foreshadowing: Each installment foreshadows future events in small ways.

Glamour: In Blame, Nightmare Moon's striking appearance and natural intimidation is explained as the effects of a mantle Luna wore, which originally belonged to the princesses' mother. Celestia wears one all the time, and its effects are so powerful even Luna can't fully resist its thrall — something which causes her no end of frustration.

The Magnificent: Parodied in Treasure, where Trixie is frequently described not just as The Great and Powerful, but in terms suited to her current state, such as The Typical and Commonplace or The Shaky and Anxious.

Malfunction Malady: Trixie's use of the Regalia of the Daymare to punish Ponyville for the end of her career almost killed her.

Mafia Princess: Muffins reveals Gilda the Griffon as one. By the end, she's implied to be taking over her late Uncle's business.

Revised Ending: Originally, the Pegasi ended up as an Official Couple by the end of Spellbound. After readers expressed their concern about the circumstances behind this, however, Saddlesoap Opera went back and tweaked the story so that Dash admits she was under the influence and Fluttershy accepts that, returning to a strong friendship.

Revenge Before Reason: Trixie's need to get payback for "Boast Busters" leads her to steal from Celestia and halfway kill herself using an Empathic Weapon that backfires on her with nearly lethal results.

Revenge by Proxy: Unable to direct her full anger at her sister thanks to her Mantle preventing it, Luna instead gleefully steps up to break the Awful Truth to her perceived replacement Twilight.

Secret Keeper: Rainbow Dash becomes one for Pinkie Pie, and Twilight for Rarity, both against their will.

Muffins reveals that Rarity knows about Ditzy dyeing her mane blonde, and Ditzy becomes one for The Doctor.

Speech Impediment: Muffins introduces a griffon with a cracked beak, giving him a permanent lisp.

Tall Poppy Syndrome: According to Loss, Rarity lives in constant fear of this, which is why she's generous to the point of driving herself deep into debt.

Tarot Motifs: Celestia uses one combined with a Themed Tarot Deck to give Twilight greater insight into her friends and explain how to help them.

There Are No Therapists: According to Spellbound, it seems the Magic-bearer's role is to play psychologist and keep the other bearers from going insane.

Written by the Winners: In Alicorns: Blame, it's revealed that Luna wasn't banished for trying to make the night last forever…Instead, it was because she made the Everfree Forest free, with all the beauty and horror of nature unleashed.

Voodoo Shark: The idea that the Elements of Harmony drives the bearers mad only affects Applejack. The rest are explained by outside sources (Fluttershy's problem is hereditary, for instance), and it comes off as something Luna made up to hurt Twilight.

One could argue otherwise. Rarity, who has the Element of Generosity, became so generous to the point of suffering massive debts, out of a fear of being rejected if she stopped putting others' needs ahead of her own. It's possible that her Element somehow made her think that, or made an already-existing fear into a bigger deal than it actually was. Pinkie, having Laughter, puts on a Stepford Smiler act even when she's not in the mood to laugh at all. Again, it's possible that her Element had something to do with her depression.

Its sequel, Secrets and Lies, also contains examples of:

Screwball: "You Screwheads are all the same; underestimating the big, dumb Mudhooves who grow your food and pull your carts and take out your trash. Well, Buzzards mighta got the wings, and you mighta got the horns, but we…GOT EVERYTHING ELSE!"

Did I Just Say That Out Loud?: Appears with a twist in Chapter 7: a side effect of Rarity dispelling the dresses is that everypony blurts out some innermost doubts and thoughts…those of somepony close to them.

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